Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

He, Zhili; Nostrand, Joy D. Van; Deng, Ye; Zhou, Jizhong

doi:10.1007/s11783-011-0301-y

Cited by 38 publications

(29 citation statements)

References 111 publications

(237 reference statements)

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“…In soils, functional microarrays or GeoChip that target specific microbial functions have been successfully used to determine the metabolic potential of the microbial communities (He et al, 2007(He et al, , 2011Bai et al, 2013;Zhang et al, 2013). A drawback of the GeoChip is the fact that novel functions and transcripts cannot be identified, and one is biased to the probes present in the chip (Dugat-Bony et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (Po0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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Section: Discussionmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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“…The labeled genomic DNA was purified using the QIAquick purification kit (Qiagen), according the manufacturer's instructions, and then dried in a SpeedVac at 45°C for 45 min (Thermo Savant). Labeled genomic DNA was hybridized on the GeoChip 4.0 microarray, as previously described (48,49). Data normalization and quality filtering were performed in multiple steps (34,48).…”

Section: Methodsmentioning

confidence: 99%

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Sun

Santalahti

Pumpanen

et al. 2015

Appl Environ Microbiol

126

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Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics. Boreal forest soils play an important role in the global carbon cycle (1) and are a net sink for atmospheric CO 2 (2, 3). Approximately 16% of the terrestrial carbon (C) stock is estimated to be stored in the boreal forest ecosystem (1). Fire is a natural disturbance in most forest ecosystems (4), and about 1% of the boreal forest burns annually (5). The frequency of forest fires in the northern boreal zone is expected to increase because of rising temperatures and more frequent dry periods resulting from ongoing climate change (6).Soil microbes perform essential ecological functions in forested ecosystems via nutrient cycling and decomposition of organic matter. Microbial activities control the turnover of organic C in soil and thus contribute to global C cycling (7). Fungi are the predominant decomposers in boreal soils and play a central role in the turnover of carbon and nitrogen (8). Ectomycorrhizal fungi form symbioses with both trees and ground vegetation in boreal forests. Many species of ground vegetation can additionally form symbioses with ericoid mycorrhizal fungi. Boreal forest ecosystem productivity is linked to plant nutrient acquisition from the microbial community via soil organic matter (SOM) decomposition. Forest fires result in the loss of mycorrhizal host plants and may modify the SOM chemistry, leading to dramatic changes in soil microbial activity (9, 10). Fire disturbance often increases soil pH and causes changes in soil temperature due to loss of canopy cover, bo...

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“…Various types of functional gene arrays have been developed for analyzing microbial community structure (He et al, 2011). For example, GeoChip 4.0 contains B83 992 probes and targets B142 000 genes from 410 functional gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, antibiotic resistance, virulence factors and bacterial phagemediated lysis (Tu et al, 2014a).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

et al. 2014

The ISME Journal

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150

126

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Determining the composition and function of subgingival dental plaque is crucial to understanding human periodontal health and disease, but it is challenging because of the complexity of the interactions between human microbiomes and human body. Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array (a combination of GeoChip 4.0 for biogeochemical processes and HuMiChip 1.0 for human microbiomes). Our analyses indicated that the phylogenetic and functional gene structure of the oral microbiomes were distinctly different between periodontal and healthy groups. Also, 16S rRNA gene sequencing analysis indicated that 39 genera were significantly different between healthy and periodontitis groups, and Fusobacterium, Porphyromonas, Treponema, Filifactor, Eubacterium, Tannerella, Hallella, Parvimonas, Peptostreptococcus and Catonella showed higher relative abundances in the periodontitis group. In addition, functional gene array data showed that a lower gene number but higher signal intensity of major genes existed in periodontitis, and a variety of genes involved in virulence factors, amino acid metabolism and glycosaminoglycan and pyrimidine degradation were enriched in periodontitis, suggesting their potential importance in periodontal pathogenesis. However, the genes involved in amino acid synthesis and pyrimidine synthesis exhibited a significantly lower relative abundance compared with healthy group. Overall, this study provides new insights into our understanding of phylogenetic and functional gene structure of subgingival microbial communities of periodontal patients and their importance in pathogenesis of periodontitis.

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Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

Cited by 38 publications

References 111 publications

Rhizosphere microbiome assemblage is affected by plant development

Rhizosphere microbiome assemblage is affected by plant development

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients

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